BDI analysis
Peter Kamerman, Tory Madden, and Antonia Wadley
25 October 2017
Import data
# Read in bdi data
bdi <- readr::read_rds('./data/bdi.rds') %>%
arrange(ID) %>%
mutate(ID = stringr::str_to_lower(ID))
# Read in site and group info
foo <- readr::read_rds('./data/demographics.rds') %>%
select(ID, Site, Group, Sex) %>%
rename(ID2 = ID) %>%
arrange(ID2)
# Join the two datasets
bdi <- foo %>%
bind_cols(bdi) %>%
rowwise() %>%
mutate(ID_match = ifelse(ID2 == ID,
yes = TRUE,
no = FALSE))
# Check for mismatches from join
nrow(filter(bdi, ID_match == FALSE))## [1] 0# Eliminate extra ID column
bdi <- bdi %>%
select(-ID,
-ID_match) %>%
rename(ID = ID2)Quick look
glimpse(bdi)## Observations: 160
## Variables: 130
## $ ID <chr> "j1", "j10", "j11", "j12", "j17", "j18", "j1...
## $ Site <chr> "u1", "u1", "u1", "u1", "u1", "u1", "u1", "u...
## $ Group <chr> "p", "t", "p", "t", "t", "t", "t", "p", "t",...
## $ Sex <chr> "female", "male", "female", "female", "femal...
## $ Sadness_BL <int> 1, 1, 3, 0, 3, NA, 0, 2, 0, 1, NA, 3, 3, 3, ...
## $ Sadness_Wk4 <int> NA, 0, 0, NA, NA, NA, 0, NA, 0, 2, NA, NA, N...
## $ Sadness_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 3, 0, 1, NA, NA, NA,...
## $ Sadness_Wk12 <int> NA, 0, 0, 0, 3, NA, NA, NA, 0, 1, NA, NA, NA...
## $ Sadness_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 1, 0, 0, NA, NA, N...
## $ Sadness_Wk48 <int> NA, 1, NA, 0, NA, NA, NA, 0, NA, 3, NA, NA, ...
## $ Pessimism_BL <int> 2, 0, 0, 1, 2, NA, 0, 3, 0, 1, NA, 3, 3, 0, ...
## $ Pessimism_Wk4 <int> NA, 0, 0, NA, NA, NA, 0, NA, 2, 1, NA, NA, N...
## $ Pessimism_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 1, 0, 1, NA, NA, NA,...
## $ Pessimism_Wk12 <int> NA, 0, 0, 0, 3, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Pessimism_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 0, 0, 0, NA, NA, N...
## $ Pessimism_Wk48 <int> NA, 0, NA, 0, NA, NA, NA, 0, NA, 1, NA, NA, ...
## $ Past_fail_BL <int> 2, 0, 2, 0, 0, NA, 2, 3, 0, 0, NA, 3, 3, 0, ...
## $ Past_fail_Wk4 <int> NA, 0, 0, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Past_fail_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 2, 0, 0, NA, NA, NA,...
## $ Past_fail_Wk12 <int> NA, 0, 0, 0, 3, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Past_fail_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 3, 0, 0, NA, NA, N...
## $ Past_fail_Wk48 <int> NA, 0, NA, 0, NA, NA, NA, 0, NA, 0, NA, NA, ...
## $ Loss_pleas_BL <int> 2, 1, 2, 1, 0, NA, 3, 1, 1, 0, NA, 2, 3, 2, ...
## $ Loss_pleas_Wk4 <int> NA, 1, 2, NA, NA, NA, 3, NA, 0, 0, NA, NA, N...
## $ Loss_pleas_Wk8 <int> NA, 1, 2, 1, NA, NA, 3, 1, 0, 0, NA, NA, NA,...
## $ Loss_pleas_Wk12 <int> NA, 0, 2, 1, 2, NA, NA, NA, 1, 0, NA, NA, NA...
## $ Loss_pleas_Wk24 <int> NA, 1, NA, 1, NA, NA, NA, 2, 1, 1, NA, NA, N...
## $ Loss_pleas_Wk48 <int> NA, 1, NA, 2, NA, NA, NA, 2, NA, 1, NA, NA, ...
## $ Guilty_BL <int> 2, 0, 2, 0, 0, NA, 1, 1, 0, 1, NA, 3, 1, 0, ...
## $ Guilty_Wk4 <int> NA, 1, 0, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Guilty_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 1, 0, 0, NA, NA, NA,...
## $ Guilty_Wk12 <int> NA, 0, 0, 0, 2, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Guilty_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 2, 0, 0, NA, NA, N...
## $ Guilty_Wk48 <int> NA, 0, NA, 0, NA, NA, NA, 0, NA, 0, NA, NA, ...
## $ Punish_BL <int> 3, 0, 3, 0, 0, NA, 0, 3, 0, 0, NA, 3, 3, 0, ...
## $ Punish_Wk4 <int> NA, 0, 0, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Punish_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 3, 0, 0, NA, NA, NA,...
## $ Punish_Wk12 <int> NA, 0, 0, 0, 3, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Punish_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 3, 0, 0, NA, NA, N...
## $ Punish_Wk48 <int> NA, 0, NA, 3, NA, NA, NA, 0, NA, 0, NA, NA, ...
## $ Self_dislike_BL <int> 1, 0, 2, 0, 0, NA, 2, 2, 1, 0, NA, 2, 3, 0, ...
## $ Self_dislike_Wk4 <int> NA, 0, 0, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Self_dislike_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 0, 0, 0, NA, NA, NA,...
## $ Self_dislike_Wk12 <int> NA, 0, 0, 0, 1, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Self_dislike_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 2, 0, 0, NA, NA, N...
## $ Self_dislike_Wk48 <int> NA, 0, NA, 1, NA, NA, NA, 0, NA, 0, NA, NA, ...
## $ Self_crit_BL <int> 3, 0, 3, 0, 3, NA, 3, 3, 0, 2, NA, 3, 3, 0, ...
## $ Self_crit_Wk4 <int> NA, 1, 0, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Self_crit_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 3, 0, 0, NA, NA, NA,...
## $ Self_crit_Wk12 <int> NA, 0, 0, 0, 3, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Self_crit_Wk24 <int> NA, 1, NA, 0, NA, NA, NA, 2, 1, 0, NA, NA, N...
## $ Self_crit_Wk48 <int> NA, 0, NA, 1, NA, NA, NA, 0, NA, 0, NA, NA, ...
## $ Suicide_BL <int> 3, 0, 0, 0, 0, NA, 0, 0, 0, 0, NA, 1, 0, 0, ...
## $ Suicide_Wk4 <int> NA, 0, 0, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Suicide_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 0, 0, 0, NA, NA, NA,...
## $ Suicide_Wk12 <int> NA, 0, 0, 0, 0, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Suicide_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 0, 0, 0, NA, NA, N...
## $ Suicide_Wk48 <int> NA, 0, NA, 0, NA, NA, NA, 0, NA, 0, NA, NA, ...
## $ Crying_BL <int> 3, 0, 3, 0, 3, NA, 0, 2, 0, 0, NA, 1, 0, 1, ...
## $ Crying_Wk4 <int> NA, 3, 0, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Crying_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 0, 0, 0, NA, NA, NA,...
## $ Crying_Wk12 <int> NA, 3, 0, 0, 3, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Crying_Wk24 <int> NA, 3, NA, 0, NA, NA, NA, 2, 3, 3, NA, NA, N...
## $ Crying_Wk48 <int> NA, 0, NA, 2, NA, NA, NA, 0, NA, 0, NA, NA, ...
## $ Agitation_BL <int> 3, 3, 3, 0, 3, NA, 3, 2, 0, 0, NA, 1, 0, 2, ...
## $ Agitation_Wk4 <int> NA, 3, 3, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Agitation_Wk8 <int> NA, 3, 0, 0, NA, NA, 0, 3, 3, 0, NA, NA, NA,...
## $ Agitation_Wk12 <int> NA, 3, 2, 3, 1, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Agitation_Wk24 <int> NA, 3, NA, 0, NA, NA, NA, 1, 3, 2, NA, NA, N...
## $ Agitation_Wk48 <int> NA, 3, NA, 2, NA, NA, NA, 2, NA, 1, NA, NA, ...
## $ Loss_int_BL <int> 3, 0, 0, 0, 0, NA, 0, 1, 0, 0, NA, 1, 0, 0, ...
## $ Loss_int_Wk4 <int> NA, 0, 0, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Loss_int_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 0, 0, 0, NA, NA, NA,...
## $ Loss_int_Wk12 <int> NA, 0, 0, 0, 1, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Loss_int_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 0, 0, 0, NA, NA, N...
## $ Loss_int_Wk48 <int> NA, 0, NA, 1, NA, NA, NA, 0, NA, 0, NA, NA, ...
## $ Indecis_BL <int> 2, 0, 0, 0, 0, NA, 0, 3, 0, 1, NA, 2, 3, 1, ...
## $ Indecis_Wk4 <int> NA, 0, 0, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Indecis_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 0, 0, 0, NA, NA, NA,...
## $ Indecis_Wk12 <int> NA, 0, 0, 0, 0, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Indecis_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 2, 0, 0, NA, NA, N...
## $ Indecis_Wk48 <int> NA, 0, NA, 1, NA, NA, NA, 0, NA, 2, NA, NA, ...
## $ Worthless_BL <int> 2, 1, 0, 0, 0, NA, 0, 2, 0, 0, NA, 3, 2, 0, ...
## $ Worthless_Wk4 <int> NA, 0, 1, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Worthless_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 0, 0, 0, NA, NA, NA,...
## $ Worthless_Wk12 <int> NA, 0, 0, 0, 0, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Worthless_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 1, 0, 0, NA, NA, N...
## $ Worthless_Wk48 <int> NA, 0, NA, 2, NA, NA, NA, 0, NA, 0, NA, NA, ...
## $ Loss_energy_BL <int> 1, 1, 2, 0, 2, NA, 0, 2, 2, 1, NA, 1, 2, 0, ...
## $ Loss_energy_Wk4 <int> NA, 1, 2, NA, NA, NA, 0, NA, 1, 0, NA, NA, N...
## $ Loss_energy_Wk8 <int> NA, 1, 2, 0, NA, NA, 0, 0, 1, 0, NA, NA, NA,...
## $ Loss_energy_Wk12 <int> NA, 1, 3, 1, 3, NA, NA, NA, 1, 1, NA, NA, NA...
## $ Loss_energy_Wk24 <int> NA, 0, NA, 1, NA, NA, NA, 1, 1, 3, NA, NA, N...
## $ Loss_energy_Wk48 <int> NA, 0, NA, 1, NA, NA, NA, 0, NA, 1, NA, NA, ...
## $ Sleep_BL <int> 3, 2, 3, 2, 2, NA, 0, 3, 3, 2, NA, 0, 2, 2, ...
## $ Sleep_Wk4 <int> NA, 3, 2, NA, NA, NA, 3, NA, 3, 2, NA, NA, N...
## $ Sleep_Wk8 <int> NA, 3, 2, 2, NA, NA, 2, 2, 2, 2, NA, NA, NA,...
## $ Sleep_Wk12 <int> NA, 3, 3, 2, 2, NA, NA, NA, 3, 3, NA, NA, NA...
## $ Sleep_Wk24 <int> NA, 2, NA, 2, NA, NA, NA, 2, 3, 2, NA, NA, N...
## $ Sleep_Wk48 <int> NA, 2, NA, 3, NA, NA, NA, 0, NA, 0, NA, NA, ...
## $ Irrit_BL <int> 2, 0, 1, 0, 2, NA, 0, 1, 2, 0, NA, 3, 3, 1, ...
## $ Irrit_Wk4 <int> NA, 0, 0, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Irrit_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 0, 0, 0, NA, NA, NA,...
## $ Irrit_Wk12 <int> NA, 0, 0, 0, 1, NA, NA, NA, 1, 1, NA, NA, NA...
## $ Irrit_Wk24 <int> NA, 0, NA, 1, NA, NA, NA, 0, 1, 1, NA, NA, N...
## $ Irrit_Wk48 <int> NA, 1, NA, 1, NA, NA, NA, 0, NA, 3, NA, NA, ...
## $ Appetite_BL <int> 1, 3, 3, 2, 0, NA, 0, 3, 2, 2, NA, 1, 2, 2, ...
## $ Appetite_Wk4 <int> NA, 3, 2, NA, NA, NA, 3, NA, 2, 2, NA, NA, N...
## $ Appetite_Wk8 <int> NA, 3, 2, 2, NA, NA, 3, 2, 2, 2, NA, NA, NA,...
## $ Appetite_Wk12 <int> NA, 3, 3, 2, 2, NA, NA, NA, 2, 0, NA, NA, NA...
## $ Appetite_Wk24 <int> NA, 2, NA, 2, NA, NA, NA, 3, 2, 2, NA, NA, N...
## $ Appetite_Wk48 <int> NA, 2, NA, 2, NA, NA, NA, 2, NA, 3, NA, NA, ...
## $ Concen_BL <int> 3, 0, 0, 0, 0, NA, 2, 2, 0, 1, NA, 1, 3, 0, ...
## $ Concen_Wk4 <int> NA, 0, 0, NA, NA, NA, 0, NA, 0, 1, NA, NA, N...
## $ Concen_Wk8 <int> NA, 0, 0, 1, NA, NA, 0, 0, 0, 1, NA, NA, NA,...
## $ Concen_Wk12 <int> NA, 0, 0, 0, 0, NA, NA, NA, 0, 1, NA, NA, NA...
## $ Concen_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 1, 0, 1, NA, NA, N...
## $ Concen_Wk48 <int> NA, 0, NA, 0, NA, NA, NA, 0, NA, 3, NA, NA, ...
## $ Fatigue_BL <int> 2, 0, 3, 1, 2, NA, 0, 2, 2, 0, NA, 0, 3, 1, ...
## $ Fatigue_Wk4 <int> NA, 0, 1, NA, NA, NA, 0, NA, 1, 0, NA, NA, N...
## $ Fatigue_Wk8 <int> NA, 0, 2, 1, NA, NA, 0, 0, 3, 1, NA, NA, NA,...
## $ Fatigue_Wk12 <int> NA, 0, 3, 0, 2, NA, NA, NA, 1, 1, NA, NA, NA...
## $ Fatigue_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 2, 0, 1, NA, NA, N...
## $ Fatigue_Wk48 <int> NA, 1, NA, 2, NA, NA, NA, 0, NA, 2, NA, NA, ...
## $ Int_sex_BL <int> 2, 1, 3, 1, 0, NA, 3, 2, 0, 1, NA, 1, 3, 2, ...
## $ Int_sex_Wk4 <int> NA, 1, 3, NA, NA, NA, 3, NA, 1, 1, NA, NA, N...
## $ Int_sex_Wk8 <int> NA, 1, 0, 1, NA, NA, 3, 0, 1, 1, NA, NA, NA,...
## $ Int_sex_Wk12 <int> NA, 1, 3, 1, 3, NA, NA, NA, 1, 1, NA, NA, NA...
## $ Int_sex_Wk24 <int> NA, 1, NA, 1, NA, NA, NA, 1, 1, 1, NA, NA, N...
## $ Int_sex_Wk48 <int> NA, 1, NA, 1, NA, NA, NA, 0, NA, 1, NA, NA, ...head(bdi)tail(bdi)Process data
Calculate total BDI scores
# Create new column (total BDI score for each time point) by summing
# scores for each time point
bdi_BL <- bdi %>% select(contains('BL'))
bdi$total_BL <- rowSums(bdi_BL)
bdi_Wk4 <- bdi %>% select(matches('Wk4$'))
bdi$total_Wk4 <- rowSums(bdi_Wk4)
bdi_Wk8 <- bdi %>% select(contains('Wk8'))
bdi$total_Wk8 <- rowSums(bdi_Wk8)
bdi_Wk12 <- bdi %>% select(contains('Wk12'))
bdi$total_Wk12 <- rowSums(bdi_Wk12)
bdi_Wk24 <- bdi %>% select(contains('Wk24'))
bdi$total_Wk24 <- rowSums(bdi_Wk24)
bdi_Wk48 <- bdi %>% select(contains('Wk48'))
bdi$total_Wk48 <- rowSums(bdi_Wk48)
# Check
glimpse(bdi)## Observations: 160
## Variables: 136
## $ ID <chr> "j1", "j10", "j11", "j12", "j17", "j18", "j1...
## $ Site <chr> "u1", "u1", "u1", "u1", "u1", "u1", "u1", "u...
## $ Group <chr> "p", "t", "p", "t", "t", "t", "t", "p", "t",...
## $ Sex <chr> "female", "male", "female", "female", "femal...
## $ Sadness_BL <int> 1, 1, 3, 0, 3, NA, 0, 2, 0, 1, NA, 3, 3, 3, ...
## $ Sadness_Wk4 <int> NA, 0, 0, NA, NA, NA, 0, NA, 0, 2, NA, NA, N...
## $ Sadness_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 3, 0, 1, NA, NA, NA,...
## $ Sadness_Wk12 <int> NA, 0, 0, 0, 3, NA, NA, NA, 0, 1, NA, NA, NA...
## $ Sadness_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 1, 0, 0, NA, NA, N...
## $ Sadness_Wk48 <int> NA, 1, NA, 0, NA, NA, NA, 0, NA, 3, NA, NA, ...
## $ Pessimism_BL <int> 2, 0, 0, 1, 2, NA, 0, 3, 0, 1, NA, 3, 3, 0, ...
## $ Pessimism_Wk4 <int> NA, 0, 0, NA, NA, NA, 0, NA, 2, 1, NA, NA, N...
## $ Pessimism_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 1, 0, 1, NA, NA, NA,...
## $ Pessimism_Wk12 <int> NA, 0, 0, 0, 3, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Pessimism_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 0, 0, 0, NA, NA, N...
## $ Pessimism_Wk48 <int> NA, 0, NA, 0, NA, NA, NA, 0, NA, 1, NA, NA, ...
## $ Past_fail_BL <int> 2, 0, 2, 0, 0, NA, 2, 3, 0, 0, NA, 3, 3, 0, ...
## $ Past_fail_Wk4 <int> NA, 0, 0, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Past_fail_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 2, 0, 0, NA, NA, NA,...
## $ Past_fail_Wk12 <int> NA, 0, 0, 0, 3, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Past_fail_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 3, 0, 0, NA, NA, N...
## $ Past_fail_Wk48 <int> NA, 0, NA, 0, NA, NA, NA, 0, NA, 0, NA, NA, ...
## $ Loss_pleas_BL <int> 2, 1, 2, 1, 0, NA, 3, 1, 1, 0, NA, 2, 3, 2, ...
## $ Loss_pleas_Wk4 <int> NA, 1, 2, NA, NA, NA, 3, NA, 0, 0, NA, NA, N...
## $ Loss_pleas_Wk8 <int> NA, 1, 2, 1, NA, NA, 3, 1, 0, 0, NA, NA, NA,...
## $ Loss_pleas_Wk12 <int> NA, 0, 2, 1, 2, NA, NA, NA, 1, 0, NA, NA, NA...
## $ Loss_pleas_Wk24 <int> NA, 1, NA, 1, NA, NA, NA, 2, 1, 1, NA, NA, N...
## $ Loss_pleas_Wk48 <int> NA, 1, NA, 2, NA, NA, NA, 2, NA, 1, NA, NA, ...
## $ Guilty_BL <int> 2, 0, 2, 0, 0, NA, 1, 1, 0, 1, NA, 3, 1, 0, ...
## $ Guilty_Wk4 <int> NA, 1, 0, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Guilty_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 1, 0, 0, NA, NA, NA,...
## $ Guilty_Wk12 <int> NA, 0, 0, 0, 2, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Guilty_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 2, 0, 0, NA, NA, N...
## $ Guilty_Wk48 <int> NA, 0, NA, 0, NA, NA, NA, 0, NA, 0, NA, NA, ...
## $ Punish_BL <int> 3, 0, 3, 0, 0, NA, 0, 3, 0, 0, NA, 3, 3, 0, ...
## $ Punish_Wk4 <int> NA, 0, 0, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Punish_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 3, 0, 0, NA, NA, NA,...
## $ Punish_Wk12 <int> NA, 0, 0, 0, 3, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Punish_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 3, 0, 0, NA, NA, N...
## $ Punish_Wk48 <int> NA, 0, NA, 3, NA, NA, NA, 0, NA, 0, NA, NA, ...
## $ Self_dislike_BL <int> 1, 0, 2, 0, 0, NA, 2, 2, 1, 0, NA, 2, 3, 0, ...
## $ Self_dislike_Wk4 <int> NA, 0, 0, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Self_dislike_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 0, 0, 0, NA, NA, NA,...
## $ Self_dislike_Wk12 <int> NA, 0, 0, 0, 1, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Self_dislike_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 2, 0, 0, NA, NA, N...
## $ Self_dislike_Wk48 <int> NA, 0, NA, 1, NA, NA, NA, 0, NA, 0, NA, NA, ...
## $ Self_crit_BL <int> 3, 0, 3, 0, 3, NA, 3, 3, 0, 2, NA, 3, 3, 0, ...
## $ Self_crit_Wk4 <int> NA, 1, 0, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Self_crit_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 3, 0, 0, NA, NA, NA,...
## $ Self_crit_Wk12 <int> NA, 0, 0, 0, 3, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Self_crit_Wk24 <int> NA, 1, NA, 0, NA, NA, NA, 2, 1, 0, NA, NA, N...
## $ Self_crit_Wk48 <int> NA, 0, NA, 1, NA, NA, NA, 0, NA, 0, NA, NA, ...
## $ Suicide_BL <int> 3, 0, 0, 0, 0, NA, 0, 0, 0, 0, NA, 1, 0, 0, ...
## $ Suicide_Wk4 <int> NA, 0, 0, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Suicide_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 0, 0, 0, NA, NA, NA,...
## $ Suicide_Wk12 <int> NA, 0, 0, 0, 0, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Suicide_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 0, 0, 0, NA, NA, N...
## $ Suicide_Wk48 <int> NA, 0, NA, 0, NA, NA, NA, 0, NA, 0, NA, NA, ...
## $ Crying_BL <int> 3, 0, 3, 0, 3, NA, 0, 2, 0, 0, NA, 1, 0, 1, ...
## $ Crying_Wk4 <int> NA, 3, 0, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Crying_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 0, 0, 0, NA, NA, NA,...
## $ Crying_Wk12 <int> NA, 3, 0, 0, 3, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Crying_Wk24 <int> NA, 3, NA, 0, NA, NA, NA, 2, 3, 3, NA, NA, N...
## $ Crying_Wk48 <int> NA, 0, NA, 2, NA, NA, NA, 0, NA, 0, NA, NA, ...
## $ Agitation_BL <int> 3, 3, 3, 0, 3, NA, 3, 2, 0, 0, NA, 1, 0, 2, ...
## $ Agitation_Wk4 <int> NA, 3, 3, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Agitation_Wk8 <int> NA, 3, 0, 0, NA, NA, 0, 3, 3, 0, NA, NA, NA,...
## $ Agitation_Wk12 <int> NA, 3, 2, 3, 1, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Agitation_Wk24 <int> NA, 3, NA, 0, NA, NA, NA, 1, 3, 2, NA, NA, N...
## $ Agitation_Wk48 <int> NA, 3, NA, 2, NA, NA, NA, 2, NA, 1, NA, NA, ...
## $ Loss_int_BL <int> 3, 0, 0, 0, 0, NA, 0, 1, 0, 0, NA, 1, 0, 0, ...
## $ Loss_int_Wk4 <int> NA, 0, 0, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Loss_int_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 0, 0, 0, NA, NA, NA,...
## $ Loss_int_Wk12 <int> NA, 0, 0, 0, 1, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Loss_int_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 0, 0, 0, NA, NA, N...
## $ Loss_int_Wk48 <int> NA, 0, NA, 1, NA, NA, NA, 0, NA, 0, NA, NA, ...
## $ Indecis_BL <int> 2, 0, 0, 0, 0, NA, 0, 3, 0, 1, NA, 2, 3, 1, ...
## $ Indecis_Wk4 <int> NA, 0, 0, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Indecis_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 0, 0, 0, NA, NA, NA,...
## $ Indecis_Wk12 <int> NA, 0, 0, 0, 0, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Indecis_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 2, 0, 0, NA, NA, N...
## $ Indecis_Wk48 <int> NA, 0, NA, 1, NA, NA, NA, 0, NA, 2, NA, NA, ...
## $ Worthless_BL <int> 2, 1, 0, 0, 0, NA, 0, 2, 0, 0, NA, 3, 2, 0, ...
## $ Worthless_Wk4 <int> NA, 0, 1, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Worthless_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 0, 0, 0, NA, NA, NA,...
## $ Worthless_Wk12 <int> NA, 0, 0, 0, 0, NA, NA, NA, 0, 0, NA, NA, NA...
## $ Worthless_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 1, 0, 0, NA, NA, N...
## $ Worthless_Wk48 <int> NA, 0, NA, 2, NA, NA, NA, 0, NA, 0, NA, NA, ...
## $ Loss_energy_BL <int> 1, 1, 2, 0, 2, NA, 0, 2, 2, 1, NA, 1, 2, 0, ...
## $ Loss_energy_Wk4 <int> NA, 1, 2, NA, NA, NA, 0, NA, 1, 0, NA, NA, N...
## $ Loss_energy_Wk8 <int> NA, 1, 2, 0, NA, NA, 0, 0, 1, 0, NA, NA, NA,...
## $ Loss_energy_Wk12 <int> NA, 1, 3, 1, 3, NA, NA, NA, 1, 1, NA, NA, NA...
## $ Loss_energy_Wk24 <int> NA, 0, NA, 1, NA, NA, NA, 1, 1, 3, NA, NA, N...
## $ Loss_energy_Wk48 <int> NA, 0, NA, 1, NA, NA, NA, 0, NA, 1, NA, NA, ...
## $ Sleep_BL <int> 3, 2, 3, 2, 2, NA, 0, 3, 3, 2, NA, 0, 2, 2, ...
## $ Sleep_Wk4 <int> NA, 3, 2, NA, NA, NA, 3, NA, 3, 2, NA, NA, N...
## $ Sleep_Wk8 <int> NA, 3, 2, 2, NA, NA, 2, 2, 2, 2, NA, NA, NA,...
## $ Sleep_Wk12 <int> NA, 3, 3, 2, 2, NA, NA, NA, 3, 3, NA, NA, NA...
## $ Sleep_Wk24 <int> NA, 2, NA, 2, NA, NA, NA, 2, 3, 2, NA, NA, N...
## $ Sleep_Wk48 <int> NA, 2, NA, 3, NA, NA, NA, 0, NA, 0, NA, NA, ...
## $ Irrit_BL <int> 2, 0, 1, 0, 2, NA, 0, 1, 2, 0, NA, 3, 3, 1, ...
## $ Irrit_Wk4 <int> NA, 0, 0, NA, NA, NA, 0, NA, 0, 0, NA, NA, N...
## $ Irrit_Wk8 <int> NA, 0, 0, 0, NA, NA, 0, 0, 0, 0, NA, NA, NA,...
## $ Irrit_Wk12 <int> NA, 0, 0, 0, 1, NA, NA, NA, 1, 1, NA, NA, NA...
## $ Irrit_Wk24 <int> NA, 0, NA, 1, NA, NA, NA, 0, 1, 1, NA, NA, N...
## $ Irrit_Wk48 <int> NA, 1, NA, 1, NA, NA, NA, 0, NA, 3, NA, NA, ...
## $ Appetite_BL <int> 1, 3, 3, 2, 0, NA, 0, 3, 2, 2, NA, 1, 2, 2, ...
## $ Appetite_Wk4 <int> NA, 3, 2, NA, NA, NA, 3, NA, 2, 2, NA, NA, N...
## $ Appetite_Wk8 <int> NA, 3, 2, 2, NA, NA, 3, 2, 2, 2, NA, NA, NA,...
## $ Appetite_Wk12 <int> NA, 3, 3, 2, 2, NA, NA, NA, 2, 0, NA, NA, NA...
## $ Appetite_Wk24 <int> NA, 2, NA, 2, NA, NA, NA, 3, 2, 2, NA, NA, N...
## $ Appetite_Wk48 <int> NA, 2, NA, 2, NA, NA, NA, 2, NA, 3, NA, NA, ...
## $ Concen_BL <int> 3, 0, 0, 0, 0, NA, 2, 2, 0, 1, NA, 1, 3, 0, ...
## $ Concen_Wk4 <int> NA, 0, 0, NA, NA, NA, 0, NA, 0, 1, NA, NA, N...
## $ Concen_Wk8 <int> NA, 0, 0, 1, NA, NA, 0, 0, 0, 1, NA, NA, NA,...
## $ Concen_Wk12 <int> NA, 0, 0, 0, 0, NA, NA, NA, 0, 1, NA, NA, NA...
## $ Concen_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 1, 0, 1, NA, NA, N...
## $ Concen_Wk48 <int> NA, 0, NA, 0, NA, NA, NA, 0, NA, 3, NA, NA, ...
## $ Fatigue_BL <int> 2, 0, 3, 1, 2, NA, 0, 2, 2, 0, NA, 0, 3, 1, ...
## $ Fatigue_Wk4 <int> NA, 0, 1, NA, NA, NA, 0, NA, 1, 0, NA, NA, N...
## $ Fatigue_Wk8 <int> NA, 0, 2, 1, NA, NA, 0, 0, 3, 1, NA, NA, NA,...
## $ Fatigue_Wk12 <int> NA, 0, 3, 0, 2, NA, NA, NA, 1, 1, NA, NA, NA...
## $ Fatigue_Wk24 <int> NA, 0, NA, 0, NA, NA, NA, 2, 0, 1, NA, NA, N...
## $ Fatigue_Wk48 <int> NA, 1, NA, 2, NA, NA, NA, 0, NA, 2, NA, NA, ...
## $ Int_sex_BL <int> 2, 1, 3, 1, 0, NA, 3, 2, 0, 1, NA, 1, 3, 2, ...
## $ Int_sex_Wk4 <int> NA, 1, 3, NA, NA, NA, 3, NA, 1, 1, NA, NA, N...
## $ Int_sex_Wk8 <int> NA, 1, 0, 1, NA, NA, 3, 0, 1, 1, NA, NA, NA,...
## $ Int_sex_Wk12 <int> NA, 1, 3, 1, 3, NA, NA, NA, 1, 1, NA, NA, NA...
## $ Int_sex_Wk24 <int> NA, 1, NA, 1, NA, NA, NA, 1, 1, 1, NA, NA, N...
## $ Int_sex_Wk48 <int> NA, 1, NA, 1, NA, NA, NA, 0, NA, 1, NA, NA, ...
## $ total_BL <dbl> 46, 13, 38, 8, 22, NA, 19, 43, 13, 13, NA, 3...
## $ total_Wk4 <dbl> NA, 17, 16, NA, NA, NA, 12, NA, 10, 9, NA, N...
## $ total_Wk8 <dbl> NA, 12, 10, 8, NA, NA, 11, 21, 12, 9, NA, NA...
## $ total_Wk12 <dbl> NA, 14, 19, 10, 38, NA, NA, NA, 10, 9, NA, N...
## $ total_Wk24 <dbl> NA, 13, NA, 8, NA, NA, NA, 31, 16, 17, NA, N...
## $ total_Wk48 <dbl> NA, 12, NA, 25, NA, NA, NA, 6, NA, 21, NA, N...Clean data
# Gather from wide format into long format
bdi <- bdi %>%
tidyr::gather(key = bdi_question,
value = bdi_rating,
-ID, - Site, - Group, -Sex)
# Separate by date
bdi <- bdi %>%
mutate(bdi_question = stringr::str_replace_all(bdi_question,
pattern = 'Int_s',
replacement = 'S'),
bdi_question = stringr::str_replace_all(bdi_question,
pattern = 'Past_f',
replacement = 'PF'),
bdi_question = stringr::str_replace_all(bdi_question,
pattern = 'Loss_p',
replacement = 'LP'),
bdi_question = stringr::str_replace_all(bdi_question,
pattern = 'Self_d',
replacement = 'SD'),
bdi_question = stringr::str_replace_all(bdi_question,
pattern = 'Self_c',
replacement = 'SC'),
bdi_question = stringr::str_replace_all(bdi_question,
pattern = 'Loss_i',
replacement = 'LI'),
bdi_question = stringr::str_replace_all(bdi_question,
pattern = 'Loss_e',
replacement = 'LE')) %>%
separate(bdi_question, c('question', 'time_point'), sep = '_')
# Set levels for time_points
bdi <- bdi %>% mutate(time_point = factor(time_point,
levels = c('BL', 'Wk4', 'Wk8',
'Wk12', 'Wk24', 'Wk48'),
ordered = TRUE))
# Get totals
bdi_tot <- filter(bdi, question == 'total')
glimpse(bdi_tot)## Observations: 960
## Variables: 7
## $ ID <chr> "j1", "j10", "j11", "j12", "j17", "j18", "j19", "j2...
## $ Site <chr> "u1", "u1", "u1", "u1", "u1", "u1", "u1", "u1", "u1...
## $ Group <chr> "p", "t", "p", "t", "t", "t", "t", "p", "t", "t", "...
## $ Sex <chr> "female", "male", "female", "female", "female", "fe...
## $ question <chr> "total", "total", "total", "total", "total", "total...
## $ time_point <ord> BL, BL, BL, BL, BL, BL, BL, BL, BL, BL, BL, BL, BL,...
## $ bdi_rating <dbl> 46, 13, 38, 8, 22, NA, 19, 43, 13, 13, NA, 38, 45, ...Plots
Note: Clinical cut-off points are marked by lines
# Create new column with time
bdi_tot <- bdi_tot %>%
mutate(Week = case_when(
stringr::str_detect(.$time_point, "Wk48") ~ 48,
stringr::str_detect(.$time_point, "BL") ~ 0,
stringr::str_detect(.$time_point, "Wk4$") ~ 4,
stringr::str_detect(.$time_point, "Wk8") ~ 8,
stringr::str_detect(.$time_point, "Wk12") ~ 12,
stringr::str_detect(.$time_point, "Wk24") ~ 24
))
# Check column contents
unique(bdi_tot$Week) ## [1] 0 4 8 12 24 48# Delete time_point column
bdi_tot <- bdi_tot %>% select(-time_point)Spaghetti plots
ggplot(data = bdi_tot) +
aes(x = Week,
y = bdi_rating,
colour = Site,
group = ID) %>%
geom_line() +
labs(title = 'Beck depression inventory',
subtitle = 'Colour by site') +
theme(legend.position = 'right') +
scale_x_continuous(breaks = c(0,4,8,12,24,48),
limits = c(0,48)) +
geom_hline(yintercept = c(10, 16, 20, 30, 40), size = 0.25, linetype = 2)
ggplot(data = bdi_tot) +
aes(x = Week,
y = bdi_rating,
colour = ID,
group = ID) %>%
geom_line() +
facet_grid(Site ~ .) +
labs(title = 'Beck depression inventory',
subtitle = 'Facet by site, colour by ID') +
theme(legend.position = 'none') +
scale_x_continuous(breaks = c(0,4,8,12,24,48),
limits = c(0,48)) +
geom_hline(yintercept = c(10, 16, 20, 30, 40), size = 0.25, linetype = 2)
ggplot(data = bdi_tot) +
aes(x = Week,
y = bdi_rating,
colour = Sex,
group = ID) %>%
geom_line() +
labs(title = 'Beck depression inventory',
subtitle = 'Colour by gender') +
theme(legend.position = 'right') +
scale_x_continuous(breaks = c(0,4,8,12,24,48),
limits = c(0,48)) +
geom_hline(yintercept = c(10, 16, 20, 30, 40), size = 0.25, linetype = 2)
bdi_tot %>% filter(Site == 'u1') %>%
ggplot(.) +
aes(x = Week,
y = bdi_rating,
colour = Group,
group = ID) %>%
geom_line() +
facet_grid(Site ~ .) +
labs(title = 'Site J: Beck depression inventory',
subtitle = 'Colour by Group') +
theme(legend.position = 'right') +
scale_x_continuous(breaks = c(0,4,8,12,24,48),
limits = c(0,48)) +
geom_hline(yintercept = c(10, 16, 20, 30, 40), size = 0.25, linetype = 2) 
bdi_tot %>% filter(Site == 'u1') %>%
ggplot(.) +
aes(x = Week,
y = bdi_rating,
colour = ID,
group = ID) %>%
geom_line() +
facet_grid(Site ~ .) +
labs(title = 'Site J: Beck depression inventory',
subtitle = 'Colour by ID') +
theme(legend.position = 'none') +
scale_x_continuous(breaks = c(0,4,8,12,24,48),
limits = c(0,48)) +
geom_hline(yintercept = c(10, 16, 20, 30, 40), size = 0.25, linetype = 2) 
bdi_tot %>% filter(Site == 'r1') %>%
ggplot(.) +
aes(x = Week,
y = bdi_rating,
colour = Group,
group = ID) %>%
geom_line() +
facet_grid(Site ~ .) +
labs(title = 'Site M: Beck depression inventory',
subtitle = 'Colour by Group') +
theme(legend.position = 'right') +
scale_x_continuous(breaks = c(0,4,8,12,24,48),
limits = c(0,48)) +
geom_hline(yintercept = c(10, 16, 20, 30, 40), size = 0.25, linetype = 2) 
bdi_tot %>% filter(Site == 'r1') %>%
ggplot(.) +
aes(x = Week,
y = bdi_rating,
colour = ID,
group = ID) %>%
geom_line() +
facet_grid(Site ~ .) +
labs(title = 'Site M: Beck depression inventory',
subtitle = 'Colour by ID') +
theme(legend.position = 'none') +
scale_x_continuous(breaks = c(0,4,8,12,24,48),
limits = c(0,48)) +
geom_hline(yintercept = c(10, 16, 20, 30, 40), size = 0.25, linetype = 2) 
bdi_tot %>% filter(Site == 'u2') %>%
ggplot(.) +
aes(x = Week,
y = bdi_rating,
colour = Group,
group = ID) %>%
geom_line() +
facet_grid(Site ~ .) +
labs(title = 'Site R: Beck depression inventory',
subtitle = 'Colour by Group') +
theme(legend.position = 'right') +
scale_x_continuous(breaks = c(0,4,8,12,24,48),
limits = c(0,48)) +
geom_hline(yintercept = c(10, 16, 20, 30, 40), size = 0.25, linetype = 2) 
bdi_tot %>% filter(Site == 'u2') %>%
ggplot(.) +
aes(x = Week,
y = bdi_rating,
colour = ID,
group = ID) %>%
geom_line() +
facet_grid(Site ~ .) +
labs(title = 'Site R: Beck depression inventory',
subtitle = 'Colour by ID') +
theme(legend.position = 'none') +
scale_x_continuous(breaks = c(0,4,8,12,24,48),
limits = c(0,48)) +
geom_hline(yintercept = c(10, 16, 20, 30, 40), size = 0.25, linetype = 2) 
bdi_tot %>% filter(Site == 'r2') %>%
ggplot(.) +
aes(x = Week,
y = bdi_rating,
colour = Group,
group = ID) %>%
geom_line() +
facet_grid(Site ~ .) +
labs(title = 'Site Z: Beck depression inventory',
subtitle = 'Colour by Group') +
theme(legend.position = 'right') +
scale_x_continuous(breaks = c(0,4,8,12,24,48),
limits = c(0,48)) +
geom_hline(yintercept = c(10, 16, 20, 30, 40), size = 0.25, linetype = 2) 
bdi_tot %>% filter(Site == 'r2') %>%
ggplot(.) +
aes(x = Week,
y = bdi_rating,
colour = ID,
group = ID) %>%
geom_line() +
facet_grid(Site ~ .) +
labs(title = 'Site Z: Beck depression inventory',
subtitle = 'Colour by ID') +
theme(legend.position = 'none') +
scale_x_continuous(breaks = c(0,4,8,12,24,48),
limits = c(0,48)) +
geom_hline(yintercept = c(10, 16, 20, 30, 40), size = 0.25, linetype = 2) 
Summary plots
ggplot(data = bdi_tot) +
aes(x = as.factor(Week),
y = bdi_rating,
colour = Group,
fill = Group) %>%
geom_boxplot(alpha = 0.6) +
geom_hline(yintercept = c(10, 16, 20, 30, 40), size = 0.25, linetype = 2) +
facet_grid(Site ~ .) +
labs(title = 'Beck Depression Inventory (BDI)',
subtitle = 'Faceted by study site, coloured by group')
ggplot(data = bdi_tot) +
aes(x = as.factor(Week),
y = bdi_rating,
colour = Sex,
fill = Sex) %>%
geom_boxplot(alpha = 0.6) +
geom_hline(yintercept = c(10, 16, 20, 30, 40), size = 0.25, linetype = 2) +
facet_grid(Group ~ .) +
labs(title = 'Beck Depression Inventory (BDI)',
subtitle = 'Faceted by study group, coloured by sex')
ggplot(data = bdi_tot) +
aes(x = as.factor(Week),
y = bdi_rating,
colour = Sex,
fill = Sex) %>%
geom_boxplot(alpha = 0.6) +
geom_hline(yintercept = c(10, 16, 20, 30, 40), size = 0.25, linetype = 2) +
facet_grid(Site ~ Group) +
labs(title = 'Beck Depression Inventory (BDI)',
subtitle = 'Faceted by study site and group, coloured by sex')
ggplot(data = filter(bdi_tot, Sex == 'female')) +
aes(x = as.factor(Week),
y = bdi_rating) %>%
geom_boxplot(alpha = 0.6) +
geom_hline(yintercept = c(10, 16, 20, 30, 40), size = 0.25, linetype = 2) +
labs(title = 'Beck Depression Inventory (BDI)',
subtitle = 'Women only')
ggplot(data = filter(bdi_tot, Sex == 'female' & Site != 'u1')) +
aes(x = as.factor(Week),
y = bdi_rating) %>%
geom_boxplot(alpha = 0.6) +
geom_hline(yintercept = c(10, 16, 20, 30, 40), size = 0.25, linetype = 2) +
labs(title = 'Beck Depression Inventory (BDI)',
subtitle = 'Women only (excluding U1)')
Session information
sessionInfo()## R version 3.4.2 (2017-09-28)
## Platform: x86_64-apple-darwin15.6.0 (64-bit)
## Running under: macOS Sierra 10.12.6
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
##
## locale:
## [1] en_GB.UTF-8/en_GB.UTF-8/en_GB.UTF-8/C/en_GB.UTF-8/en_GB.UTF-8
##
## attached base packages:
## [1] stats graphics grDevices utils datasets methods base
##
## other attached packages:
## [1] bindrcpp_0.2 tidyr_0.7.2 ggplot2_2.2.1 dplyr_0.7.4
##
## loaded via a namespace (and not attached):
## [1] Rcpp_0.12.13 knitr_1.17 bindr_0.1 magrittr_1.5
## [5] hms_0.3 tidyselect_0.2.2 munsell_0.4.3 colorspace_1.3-2
## [9] R6_2.2.2 rlang_0.1.2 plyr_1.8.4 stringr_1.2.0
## [13] tools_3.4.2 grid_3.4.2 gtable_0.2.0 htmltools_0.3.6
## [17] lazyeval_0.2.0 yaml_2.1.14 assertthat_0.2.0 rprojroot_1.2
## [21] digest_0.6.12 tibble_1.3.4 reshape2_1.4.2 readr_1.1.1
## [25] purrr_0.2.4 glue_1.1.1 evaluate_0.10.1 rmarkdown_1.6
## [29] labeling_0.3 stringi_1.1.5 compiler_3.4.2 scales_0.5.0
## [33] backports_1.1.1 jsonlite_1.5 pkgconfig_2.0.1